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Epigenetics, Dietary Restriction, and Insects: Implications for Humankind

  • Ting Lian
  • Uma Gaur
  • Mingyao YangEmail author
Reference work entry

Abstract

Diet nutrition has been confirmed to influence health for decades. Proper total nutrition intake is beneficial for organisms’ health from yeast, insects, rodents, to humans. Epigenetic factors are considered to be one of the mediators of the dietary effects, which make the effects remembered from one cell generation to the next by marking on the genome. In this chapter, we will review the accumulative evidences about the association between epigenetic factors (including DNA methylation, histone modifications, and other epigenetic factors), and diet nutrition especially dietary restriction, and its implications for humankind. At the same time, we suggest that insects can be employed as efficient models to investigate the fundamental basis of human diseases especially the involvement of epigenetic mechanisms, because insects owe inexpensive cost, easy accessibility, shorter generations, along with conserved epigenetic mechanisms and signaling pathways with humans.

Keywords

Epigenetics Dietary restriction Nutrition DNA methylation Histone modifications Insect Diseases Trans-generational effects Genome 

List of Abbreviations

5mC

5-Methylcytosine

6mA

N6-Methyladenine

10-HDA

(E)-10-hydroxy-2-decenoic acid

ChIP-seq

Chromatin immunoprecipitation sequencing

DMGs

Differentiated methylated genes

Dnmts

DNA methyltransferases

DR

Dietary restriction

EGFR

Epidermal growth factor receptor

H3K27ac

Histone H3 at lysine 27

HAD

10-hydroxy-2-decenoic acid

HDAC

Histone deacetylase

HDACi

Histone deacetylase inhibitor

LC-MS/MS

Liquid chromatography coupled with tandem mass spectrometry

lnc-RNAs

Long noncoding RNAs

LPHC

Low-protein, high-carbohydrate diet

OCM

One-carbon metabolism

RJ

Royal jelly

SAM

S-adenosylmethionine

Sir2

Sirtuin-2

TEs

Transposable elements

WJ

Worker jelly

References

  1. Bauer JH, Morris SNS, Chang C et al (2009) dSir2 and Dmp53 interact to mediate aspects of CR-dependent lifespan extension in D. melanogaster. Aging (Albany NY) 1:38–48CrossRefGoogle Scholar
  2. Bayersdorfer F, Voigt A, Schneuwly S et al (2010) Dopamine-dependent neurodegeneration in Drosophila models of familial and sporadic Parkinson’s disease. Neurobiol Dis 40:113–119CrossRefGoogle Scholar
  3. Bednar J, Horowitz RA, Grigoryev SA et al (1998) Nucleosomes, linker DNA, and linker histone form a unique structural motif that directs the higher-order folding and compaction of chromatin. Proc Natl Acad Sci 95:14173–14178CrossRefGoogle Scholar
  4. Beeler SM, Wong GT, Zheng JM et al (2014) Whole-genome DNA methylation profile of the jewel wasp (Nasonia vitripennis). G3 4:383–388CrossRefGoogle Scholar
  5. Bergman P, Seyedoleslami ES, Engström Y (2016) Drosophila as a model for human diseases – focus on innate immunity in barrier epithelia. Curr Top Dev Biol. Academic 121:29–81Google Scholar
  6. Bestor TH (2000) The DNA methyltransferases of mammals. Hum Mol Genet 9:2395–2402CrossRefGoogle Scholar
  7. Bingsohn L, Knorr E, Vilcinskas A (2016) The model beetle Tribolium castaneum can be used as an early warning system for transgenerational epigenetic side effects caused by pharmaceuticals. Comp Biochem Physiol C 185–186:57–64Google Scholar
  8. Bird A (2002) DNA methylation patterns and epigenetic memory. Genes Dev 16:6–21CrossRefGoogle Scholar
  9. Boerjan B, Sas F, Emst UR et al (2011) Locust phase polyphenism: does epigenetic precede endocrine regulation? Gen Comp Endocrinol 173:120–128CrossRefGoogle Scholar
  10. Bonasio R, Li Q, Lian J et al (2012) Genome-wide and caste-specific DNA methylomes of the ants Camponotus floridanus and Harpegnathos saltator. Curr Biol 22:1755–1764CrossRefGoogle Scholar
  11. Buttstedt A, Ihling CH, Pietzsch M et al (2016) Royalactin is not a royal making of a queen. Nature 537:E10–E12CrossRefGoogle Scholar
  12. Capuano F, Mülleder M, Kok R et al (2014) Cytosine DNA methylation is found in Drosophila melanogaster but absent in Saccharomyces cerevisiae, Schizosaccharomyces pombe, and other yeast species. Anal Chem 86:3697–3702CrossRefGoogle Scholar
  13. Cedar H, Bergman Y (2009) Linking. DNA methylation and histone modification: patterns and paradigms. Nat Rev Genet 10:295–304CrossRefGoogle Scholar
  14. Chen PN, Chu SC, Kuo WH et al (2011) Epigallocatechin-3 Gallate inhibits invasion, epithelial −mesenchymal transition, and tumor growth in oral cancer cells. J Agric Food Chem 59:3836–3844CrossRefGoogle Scholar
  15. Dickman MJ, Kucharski R, Maleszka R et al (2013) Extensive histone post-translational modification in honey bees. Insect Biochem Mol Biol 43:125–137CrossRefGoogle Scholar
  16. Falckenhayn C, Boerjan B, Raddatz G et al (2013) Characterization of genome methylation patterns in the desert locust, Schistocerca gregaria. J Exp Biol 216:1423–1429CrossRefGoogle Scholar
  17. Fontana L, Partridge L (2015) Promoting health and longevity through diet: from model organisms to humans. Cell 161:106–118CrossRefGoogle Scholar
  18. Ford D (2013) Honeybees and cell lines as models of DNA methylation and aging in response to diet. Exp Gerontol 48:614–619CrossRefGoogle Scholar
  19. Foret S, Kucharski R, Pellegrini M et al (2012) DNA methylation dynamics, metabolic fluxes, gene splicing, and alternative phenotypes in honey bees. Proc Natl Acad Sci 109:4968–4973CrossRefGoogle Scholar
  20. Freitak D, Schmidtberg H, Dickel F et al (2014) The maternal transfer of bacteria can mediate trans-generational immune priming in insects. Virulence 5:547–554CrossRefGoogle Scholar
  21. Guan C, Zeng ZJ, Wang ZL et al (2013) Expression of Sir2, Hdac1 and Ash2 in Honey Bee (Apis Mellifera L.) Queens and Workers. J Apic Sci 57:67–73Google Scholar
  22. Guo S, Jiang F, Yang P et al (2016) Characteristics and expression patterns of histone-modifying enzyme systems in the migratory locust. Insect Biochem Mol Biol 76:18–28CrossRefGoogle Scholar
  23. Hoffmann J, Romey R, Fink C et al (2013) Overexpression of Sir2 in the adult fat body is sufficient to extend lifespan of male and female Drosophila. Aging (Albany NY) 5:315–327CrossRefGoogle Scholar
  24. Hu C-W, Chen J-L, Hsu Y-W et al (2015) Trace analysis of methylated and hydroxymethylated cytosines in DNA by isotope-dilution LC–MS/MS: first evidence of DNA methylation in Caenorhabditis elegans. Biochem J 465:39–47CrossRefGoogle Scholar
  25. Hunt JH, Kensinger BJ, Kossuth JA et al (2007) A diapause pathway underlies the gyne phenotype in Polistes wasps, revealing an evolutionary route to caste-containing insect societies. Proc Natl Acad Sci 104:14020–14025CrossRefGoogle Scholar
  26. Kamakura M (2011) Royalactin induces queen differentiation in honeybees. Nature 473:478–483CrossRefGoogle Scholar
  27. Kim CH, Lee EK, Choi YJ et al (2016a) Short-term calorie restriction ameliorates genomewide, age-related alterations in DNA methylation. Aging Cell 15:1074–1081CrossRefGoogle Scholar
  28. Kim D, Thairu MW, Hansen AK (2016b) Novel insights into insect-microbe interactions – role of epigenomics and small RNAs. Front Plant Sci 7:1164PubMedPubMedCentralGoogle Scholar
  29. Kucharski R, Maleszka J, Foret S et al (2008) Nutritional control of reproductive status in honeybees via DNA methylation. Science 319:1827–1830CrossRefGoogle Scholar
  30. Lee J, Hwang YJ, Kim KY et al (2013) Epigenetic mechanisms of neurodegeneration in Huntington’s disease. Neurotherapeutics 10:664–676CrossRefGoogle Scholar
  31. Liao Z, Jia Q, Li F et al (2010) Identification of two piwi genes and their expression profile in honeybee, Apis mellifera. Arch Insect Biochem 74:91–102Google Scholar
  32. Li-Byarlay H, Li Y, Stroud H et al (2013) RNA interference knockdown of DNA methyl-transferase 3 affects gene alternative splicing in the honey bee. Proc Natl Acad Sci 110:12750–12755CrossRefGoogle Scholar
  33. Lopez TE, Pham HM, Nguyen BV et al (2016) Green tea polyphenols require the mitochondrial iron transporter, mitoferrin, for lifespan extension in Drosophila melanogaster. Arch Insect Biochem 93:210–221CrossRefGoogle Scholar
  34. Lyko F, Maleszka R (2011) Insects as innovative models for functional studies of DNA methylation. Trends Genet 27:127–131CrossRefGoogle Scholar
  35. Lyko F, Ramsahoye BH, Jaenisch R (2000) Development: DNA methylation in Drosophila melanogaster. Nature 408:538–540CrossRefGoogle Scholar
  36. Lyko F, Foret S, Kucharski R et al (2010) The honey bee epigenomes: differential methylation of brain DNA in queens and workers. PLoS Biol 8:e1000506CrossRefGoogle Scholar
  37. Marhold J, Rothe N, Pauli A et al (2004) Conservation of DNA methylation in dipteran insects. Insect Mol Biol 13:117–123CrossRefGoogle Scholar
  38. Mason JB, Tang SY (2017) Folate status and colorectal cancer risk: a 2016 update. Mol Asp Med 53:73–79CrossRefGoogle Scholar
  39. Mattocks DA, Mentch SJ, Shneyder J et al (2017) Short term methionine restriction increases hepatic global DNA methylation in adult but not young male C57BL/6J mice. Exp Gerontol 88:1–8CrossRefGoogle Scholar
  40. Mukherjee K, Vilcinskas A (2014) Development and immunity-related microRNAs of the lepidopteran model host Galleria mellonella. BMC Genomics 15:1–12CrossRefGoogle Scholar
  41. Mukherjee K, Twyman RM, Vilcinskas A (2015) Insects as models to study the epigenetic basis of disease. Prog Biophys Mol Biol 118:69–78CrossRefGoogle Scholar
  42. Paoli PP, Wakeling LA, Wright GA et al (2014) The dietary proportion of essential amino acids and Sir2 influence lifespan in the honeybee. Age 36:1239–1247CrossRefGoogle Scholar
  43. Prüßing K, Voigt A, Schulz JB (2013) Drosophila melanogaster as a model organism for Alzheimer’s disease. Mol Neurodegener 8:1–12CrossRefGoogle Scholar
  44. Romanoski CE, Glass CK, Stunnenberg HG et al (2015) Epigenomics: roadmap for regulation. Nature 518:314–316CrossRefGoogle Scholar
  45. Shi YY, Huang ZY, Zeng ZJ et al (2011) Diet and cell size both affect queen-worker differentiation through DNA methylation in honey bees (Apis mellifera, Apidae). PLoS One 6:e18808CrossRefGoogle Scholar
  46. Simola DF, Ye C, Mutti NS et al (2013) A chromatin link to caste identity in the carpenter ant Camponotus floridanus. Genome Res 23:486–496CrossRefGoogle Scholar
  47. Slade JD, Staveley BE (2016) Extended longevity and survivorship during amino-acid starvation in a Drosophila Sir2 mutant heterozygote. Genome 59:311–318CrossRefGoogle Scholar
  48. Smith ZD, Meissner A (2013) DNA methylation: roles in mammalian development. Nat Rev Genet 14:204–220CrossRefGoogle Scholar
  49. Snell-Rood EC, Troth A, Moczek AP (2013) DNA methylation as a mechanism of nutritional plasticity: limited support from horned beetles. J Exp Zool Part B: Mol Devel Evol 320:22–34CrossRefGoogle Scholar
  50. Spannhoff A, Kim YK, Raynal NJM et al (2011) Histone deacetylase inhibitor activity in royal jelly might facilitate caste switching in bees. EMBO Rep 12:238–243CrossRefGoogle Scholar
  51. Sukla KK, Nagar R, Raman R (2014) Vitamin-B12 and folate deficiency, major contributing factors for anemia: a population based study. e-SPEN J 9:e45–e48CrossRefGoogle Scholar
  52. Tabunoki H, Ono H, Ode H et al (2013) Identification of key uric acid synthesis pathway in a unique mutant silkworm Bombyx mori model of Parkinson’s disease. PLoS One 8:e69130CrossRefGoogle Scholar
  53. Terrapon N, Li C, Robertson HM et al (2014) Molecular traces of alternative social organization in a termite genome. Nat Commun 5:3636CrossRefGoogle Scholar
  54. Tipping M, Perrimon N (2014) Drosophila as a model for context-dependent tumorigenesis. J Cell Physiol 229:27–33PubMedPubMedCentralGoogle Scholar
  55. Waddington CH (2012) The epigenotype. Int J Epidemiol 41:10–13CrossRefGoogle Scholar
  56. Wion D, Casadesus J (2006) N6-methyl-adenine: an epigenetic signal for DNA-protein interactions. Nat Rev Microbiol 4:183–192CrossRefGoogle Scholar
  57. Xia Q, Zhou Z, Lu C et al (2004) A draft sequence for the genome of the domesticated silkworm (Bombyx mori). Science 6:1937–1940Google Scholar
  58. Xiang H, Zhu J, Chen Q et al (2010) Single base-resolution methylome of the silkworm reveals a sparse epigenomic map. Nat Biotechnol 28:516–520CrossRefGoogle Scholar
  59. Xiong Y, Zhao K, Wu J et al (2013) HDAC6 mutations rescue human tau-induced microtubule defects in Drosophila. Proc Natl Acad Sci 110:4604–4609CrossRefGoogle Scholar
  60. Yang D, Lian T, Tu J et al (2016) LncRNA mediated regulation of aging pathways in Drosophila melanogaster during dietary restriction. Aging 8:2182–2203CrossRefGoogle Scholar
  61. Zemach A, McDaniel IE, Silva P et al (2010) Genome-wide evolutionary analysis of eukaryotic DNA methylation. Science 328:916–919CrossRefGoogle Scholar
  62. Zhang G, Huang H, Liu D et al (2015) N6-Methyladenine DNA modification in Drosophila. Cell 161:893–906CrossRefGoogle Scholar
  63. Zhou X, Oi FM, Scharf ME (2006) Social exploitation of hexamerin: RNAi reveals a major caste-regulatory factor in termites. Proc Natl Acad Sci 103:4499–4504CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Institute of Animal Genetics and BreedingSichuan Agricultural UniversityChengduChina

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